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425 lines
15 KiB
R
Executable File
425 lines
15 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Determine multidrug-resistant organisms (MDRO)
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#'
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
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#' @param x table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
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#' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
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#' @param info print progress
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#' @inheritParams eucast_rules
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#' @param verbose print additional info: missing antibiotic columns per parameter
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#' @inheritSection eucast_rules Antibiotics
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#' @details When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link}).
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#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
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#' @rdname mdro
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#' @importFrom dplyr %>%
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#' @importFrom crayon red blue bold
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' library(dplyr)
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#'
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#' septic_patients %>%
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#' mutate(EUCAST = mdro(.),
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#' BRMO = brmo(.))
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mdro <- function(x,
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country = NULL,
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col_mo = NULL,
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info = TRUE,
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verbose = FALSE,
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...) {
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tbl_ <- x
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if (!is.data.frame(tbl_)) {
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stop("`x` must be a data frame.", call. = FALSE)
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}
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(tbl = tbl_, type = "mo")
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}
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if (is.null(col_mo)) {
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stop("`col_mo` must be set.", call. = FALSE)
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}
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if (length(country) > 1) {
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stop('`country` must be a length one character string.', call. = FALSE)
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}
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if (is.null(country)) {
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country <- 'EUCAST'
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}
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country <- trimws(country)
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if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
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stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
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}
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# create list and make country code case-independent
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guideline <- list(country = list(code = tolower(country)))
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if (guideline$country$code == 'eucast') {
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guideline$country$name <- '(European guidelines)'
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guideline$name <- 'EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables"'
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guideline$version <- 'Version 3.1'
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guideline$source <- 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'
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# support per country:
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} else if (guideline$country$code == 'de') {
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guideline$country$name <- 'Germany'
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guideline$name <- ''
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guideline$version <- ''
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guideline$source <- ''
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} else if (guideline$country$code == 'nl') {
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guideline$country$name <- 'The Netherlands'
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guideline$name <- 'WIP-Richtlijn BRMO'
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guideline$version <- 'Revision as of December 2017'
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guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
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# add here more countries like this:
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# } else if (country$code == 'xx') {
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# country$name <- 'country name'
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} else {
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stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
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}
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if (info == TRUE) {
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cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
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"Guideline: ", red(paste0(guideline$name, ", ", guideline$version, "\n")),
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"Country : ", red(paste0(guideline$country$name, "\n")),
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"Source : ", blue(paste0(guideline$source, "\n")),
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"\n", sep = "")
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}
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cols_ab <- get_column_abx(tbl = x,
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...)
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AMC <- cols_ab['AMC']
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AMK <- cols_ab['AMK']
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AMP <- cols_ab['AMP']
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AMX <- cols_ab['AMX']
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ATM <- cols_ab['ATM']
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AZL <- cols_ab['AZL']
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AZM <- cols_ab['AZM']
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CAZ <- cols_ab['CAZ']
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CED <- cols_ab['CED']
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CHL <- cols_ab['CHL']
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CIP <- cols_ab['CIP']
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CLI <- cols_ab['CLI']
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CLR <- cols_ab['CLR']
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COL <- cols_ab['COL']
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CRO <- cols_ab['CRO']
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CTX <- cols_ab['CTX']
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CXM <- cols_ab['CXM']
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CZO <- cols_ab['CZO']
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DAP <- cols_ab['DAP']
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DOX <- cols_ab['DOX']
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ERY <- cols_ab['ERY']
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ETP <- cols_ab['ETP']
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FEP <- cols_ab['FEP']
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FLC <- cols_ab['FLC']
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FOS <- cols_ab['FOS']
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FOX <- cols_ab['FOX']
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FUS <- cols_ab['FUS']
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GEN <- cols_ab['GEN']
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IPM <- cols_ab['IPM']
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KAN <- cols_ab['KAN']
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LIN <- cols_ab['LIN']
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LNZ <- cols_ab['LNZ']
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LVX <- cols_ab['LVX']
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MEM <- cols_ab['MEM']
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MEZ <- cols_ab['MEZ']
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MTR <- cols_ab['MTR']
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MFX <- cols_ab['MFX']
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MNO <- cols_ab['MNO']
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NAL <- cols_ab['NAL']
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NEO <- cols_ab['NEO']
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NET <- cols_ab['NET']
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NIT <- cols_ab['NIT']
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NOR <- cols_ab['NOR']
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NOV <- cols_ab['NOV']
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OFX <- cols_ab['OFX']
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PEN <- cols_ab['PEN']
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PIP <- cols_ab['PIP']
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PLB <- cols_ab['PLB']
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PRI <- cols_ab['PRI']
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QDA <- cols_ab['QDA']
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RID <- cols_ab['RID']
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RIF <- cols_ab['RIF']
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RXT <- cols_ab['RXT']
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SIS <- cols_ab['SIS']
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SXT <- cols_ab['SXT']
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TCY <- cols_ab['TCY']
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TEC <- cols_ab['TEC']
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TGC <- cols_ab['TGC']
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TIC <- cols_ab['TIC']
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TMP <- cols_ab['TMP']
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TOB <- cols_ab['TOB']
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TZP <- cols_ab['TZP']
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VAN <- cols_ab['VAN']
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ab_missing <- function(ab) {
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isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
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}
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# antibiotic classes
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aminoglycosides <- c(TOB, GEN)
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cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
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cephalosporins_3rd <- c(CTX, CRO, CAZ)
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carbapenems <- c(ETP, IPM, MEM)
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fluoroquinolones <- c(OFX, CIP, LVX, MFX)
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# helper function for editing the table
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trans_tbl <- function(to, rows, cols, any_all) {
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cols <- cols[!ab_missing(cols)]
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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if (any_all == "any") {
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col_filter <- which(tbl_[, cols] == 'R')
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} else if (any_all == "all") {
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col_filter <- tbl_ %>%
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mutate(index = 1:nrow(.)) %>%
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filter_at(vars(cols), all_vars(. == "R")) %>%
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pull((index))
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}
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rows <- rows[rows %in% col_filter]
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tbl_[rows, 'MDRO'] <<- to
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}
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}
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tbl_ <- tbl_ %>%
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mutate_at(vars(col_mo), as.mo) %>%
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# join to microorganisms data set
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left_join_microorganisms(by = col_mo) %>%
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# add unconfirmed to where genus is available
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mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
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if (guideline$country$code == 'eucast') {
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# EUCAST ------------------------------------------------------------------
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# Table 5
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trans_tbl(3,
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which(tbl_$family == 'Enterobacteriaceae'
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| tbl_$fullname %like% '^Pseudomonas aeruginosa'
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| tbl_$genus == 'Acinetobacter'),
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COL,
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"all")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Salmonella Typhi'),
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c(carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Haemophilus influenzae'),
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c(cephalosporins_3rd, carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Moraxella catarrhalis'),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Neisseria meningitidis'),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Neisseria gonorrhoeae'),
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AZM,
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"any")
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# Table 6
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trans_tbl(3,
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which(tbl_$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
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c(VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(tbl_$genus == 'Corynebacterium'),
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c(VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Streptococcus pneumoniae'),
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c(carbapenems, VAN, TEC, DAP, LNZ, QDA, TGC, RIF),
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"any")
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trans_tbl(3, # Sr. groups A/B/C/G
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which(tbl_$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
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c(PEN, cephalosporins, VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(tbl_$genus == 'Enterococcus'),
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c(DAP, LNZ, TGC, TEC),
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Enterococcus faecalis'),
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c(AMP, AMX),
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"any")
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# Table 7
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trans_tbl(3,
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which(tbl_$genus == 'Bacteroides'),
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MTR,
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"any")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Clostridium difficile'),
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c( MTR, VAN),
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"any")
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}
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if (guideline$country$code == 'de') {
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# Germany -----------------------------------------------------------------
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stop("We are still working on German guidelines in this beta version.", call. = FALSE)
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}
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if (guideline$country$code == 'nl') {
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# Netherlands -------------------------------------------------------------
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aminoglycosides <- aminoglycosides[!ab_missing(aminoglycosides)]
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fluoroquinolones <- fluoroquinolones[!ab_missing(fluoroquinolones)]
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carbapenems <- carbapenems[!ab_missing(carbapenems)]
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# Table 1
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trans_tbl(3,
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which(tbl_$family == 'Enterobacteriaceae'),
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c(aminoglycosides, fluoroquinolones),
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"all")
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trans_tbl(2,
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which(tbl_$family == 'Enterobacteriaceae'),
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c(carbapenems),
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"any")
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# Table 2
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trans_tbl(2,
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which(tbl_$genus == 'Acinetobacter'),
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c(carbapenems),
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"any")
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trans_tbl(3,
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which(tbl_$genus == 'Acinetobacter'),
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c(aminoglycosides, fluoroquinolones),
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"all")
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trans_tbl(3,
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which(tbl_$fullname %like% '^Stenotrophomonas maltophilia'),
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SXT,
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"all")
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if (!ab_missing(MEM) & !ab_missing(IPM)
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& !ab_missing(GEN) & !ab_missing(TOB)
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& !ab_missing(CIP)
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& !ab_missing(CAZ)
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& !ab_missing(TZP) ) {
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tbl_$psae <- 0
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tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"]
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tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"]
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tbl_[which(tbl_[, CIP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CIP] == "R"), "psae"]
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tbl_[which(tbl_[, CAZ] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CAZ] == "R"), "psae"]
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tbl_[which(tbl_[, TZP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, TZP] == "R"), "psae"]
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} else {
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tbl_$psae <- 0
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}
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tbl_[which(
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tbl_$fullname %like% 'Pseudomonas aeruginosa'
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& tbl_$psae >= 3
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), 'MDRO'] <- 3
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# Table 3
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trans_tbl(3,
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which(tbl_$fullname %like% 'Streptococcus pneumoniae'),
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PEN,
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"all")
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trans_tbl(3,
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which(tbl_$fullname %like% 'Streptococcus pneumoniae'),
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VAN,
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"all")
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trans_tbl(3,
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which(tbl_$fullname %like% 'Enterococcus faecium'),
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c(PEN, VAN),
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"all")
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}
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factor(x = tbl_$MDRO,
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levels = 1:3,
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labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
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ordered = TRUE)
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}
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#' @rdname mdro
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#' @export
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brmo <- function(..., country = "nl") {
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mdro(..., country = "nl")
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}
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#' @rdname mdro
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#' @export
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mrgn <- function(x, country = "de", ...) {
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mdro(x = x, country = "de", ...)
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}
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#' @rdname mdro
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#' @export
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eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
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mdro(x = x, country = "EUCAST", ...)
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}
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# is_ESBL <- function(x, col_mo = NULL, ...) {
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# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
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# cols_ab <- get_column_abx(tbl = x,
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# soft_dependencies = c("AMX", "AMP"),
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# hard_dependencies = c("CAZ"),
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# ...)
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#
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# if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
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# # both ampicillin and amoxicillin are missing
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# generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
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# return(rep(NA, nrow(x)))
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# }
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#
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# ESBLs <- rep(NA, nrow(x))
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#
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# # first make all eligible cases FALSE
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# ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# )] <- FALSE
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# # now make the positives cases TRUE
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# ESBLs[which(!is.na(ESBLs)
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# & x[, get_ab_col(cols_ab, "AMX")] == "R"
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# & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
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# ESBLs
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#
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# }
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#
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# is_3MRGN <- function(x, ...) {
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#
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# }
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#
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# is_4MRGN <- function(x, ...) {
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#
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# }
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get_column_mo <- function(tbl, col_mo = NULL) {
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# throws a blue note about which column will be used if guessed
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(tbl = tbl, type = "mo")
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}
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if (is.null(col_mo)) {
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stop("`col_mo` must be set.", call. = FALSE)
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}
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col_mo
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}
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